QC Report


general
Report generated at2020-08-18 18:28:18
TitleBRD4_OL-Neg_Output
DescriptionChIP-seq for BRD4_OL-Neg_Output
Pipeline versionv1.3.6
Pipeline typetf
Genomehg38
Alignerbowtie2
Sequencing endedness{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}, 'ctl2': {'paired_end': False}}
Peak callerspp

Alignment quality metrics


SAMstat (raw unfiltered BAM)

rep1rep2ctl1ctl2
Total Reads25162318233664104000000040000000
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads21416235173729273875302639256995
Mapped Reads (QC-failed)0000
% Mapped Reads85.174.496.8999999999999998.1
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Marking duplicates (filtered BAM)

rep1rep2ctl1ctl2
Unpaired Reads18904733151181283299641333673357
Paired Reads0000
Unmapped Reads0000
Unpaired Duplicate Reads229234828038341572242729930
Paired Duplicate Reads0000
Paired Optical Duplicate Reads0000
% Duplicate Reads12.125818.54624.76492.1677

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1ctl2
Total Reads16612385123142943142417132943427
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads16612385123142943142417132943427
Mapped Reads (QC-failed)0000
% Mapped Reads100.0100.0100.0100.0
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Filtered and duplicates removed


Sequence quality metrics (filtered/deduped BAM)

rep1
rep1
rep2
rep2

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.


Library complexity quality metrics


Library complexity (filtered non-mito BAM)

rep1rep2ctl1ctl2
Total Fragments18898183150878353299514133667992
Distinct Fragments16661928123251573151001833060330
Positions with Two Read172873619201271371423582759
NRF = Distinct/Total0.8816680.8168940.954990.981951
PBC1 = OneRead/Distinct0.8821520.8128970.9547450.982062
PBC2 = OneRead/TwoRead8.5023735.21792421.93637155.71307

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline


NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally


Replication quality metrics


IDR (Irreproducible Discovery Rate) plots

rep1_vs_rep2
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
pooled-pr1_vs_pooled-pr2

Reproducibility QC and peak detection statistics

overlapidr
Nt9954634732
N111595645755
N24562916821
Np12160647867
N optimal12160647867
N conservative9954634732
Optimal Setpooled-pr1_vs_pooled-pr2pooled-pr1_vs_pooled-pr2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.22160609165611891.3781815040884486
Self Consistency Ratio2.541278572837452.7201117650555853
Reproducibility Testborderlineborderline

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks299970299961

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size136.0116.0134.0134.0
25 percentile544.0464.0390.0536.0
50 percentile (median)544.0464.0536.0536.0
75 percentile544.0464.0536.0536.0
Max size895.0642.02048.02048.0
Mean531.8769276927693462.9228866419301462.7303988133787506.2361067710475

rep1
rep1
rep2
rep2
idr_opt
idr_opt
overlap_opt
overlap_opt

Enrichment / Signal-to-noise ratio


Strand cross-correlation measures (trimmed/filtered SE BAM)

rep1rep2
Number of Subsampled Reads1500000015000000
Estimated Fragment Length220145
Cross-correlation at Estimated Fragment Length0.2230433070105740.143842563586747
Phantom Peak105105
Cross-correlation at Phantom Peak0.20359390.1430669
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.13900220.1250292
NSC (Normalized Strand Cross-correlation coeff.)1.6046031.150472
RSC (Relative Strand Cross-correlation coeff.)1.3011131.043003


Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.


rep1
rep1
rep2
rep2

Jensen-Shannon distance (filtered/deduped BAM)

rep1rep2
AUC0.195890335333788580.2268277432831919
Synthetic AUC0.49128634448159620.48988931529594604
X-intercept0.21024077110746710.2314862216534016
Synthetic X-intercept3.4246058163589143e-1124.906028279462881e-83
Elbow Point0.67851457825060990.5801923769147702
Synthetic Elbow Point0.51071750940159040.49615660764024844
JS Distance0.26450897836241220.14921820089347657
Synthetic JS Distance0.385923189801698260.2966816490656603
% Genome Enriched22.58988921329440631.483421989361275
Diff. Enrichment35.44134482672521430.970241686696532
CHANCE Divergence0.30513651208260330.2663707338397109

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.31827705654546290.2123475369355320.32648904257341480.180294542261212860.32625696588761730.180822059307663120.258928513708746140.26807224334074980.2680834626084613

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.162647395506411220.227375539394253150.080892741394675160.18228646295691253

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.108401278971568080.16401395705673810.0485494336906362660.1292620559726196

For spp raw peaks:


For overlap/IDR peaks: